smamp.tools module

Misc tools

Copyright 2019 Simulation Lab

University of Freiburg

Author : Lukas Elflein elfleinl@cs.uni-freiburg.de

 

""" Misc tools
Copyright 2019 Simulation Lab
University of Freiburg
Author: Lukas Elflein <elfleinl@cs.uni-freiburg.de>
"""

import os 

class cd:
    """Context manager for changing the current working directory"""
    def __init__(self, newPath):
        self.newPath = os.path.expanduser(newPath)

    def __enter__(self):
        self.savedPath = os.getcwd()
        os.chdir(self.newPath)

    def __exit__(self, etype, value, traceback):
        os.chdir(self.savedPath)

def check_existence(path, neccessary_files, verbose=True):
        """Check if all neccessary files exist in path, print warning for missing files.

        Arguments:
        path: string, the path to search
        neccessary_files: list of strings, check if they exist in path
        verbose: Bool, controls amount of printing

        Returns:
        String warning xor None 
        """
        with cd(path):
                # Files should be here
                # if verbose:
                #       print([f for s, d, f in os.walk('.')])

                for f in neccessary_files:
                        if not (os.path.islink(f) or os.path.isfile(f)):
                                warning = 'File not found: {}'.format(f)
                                if verbose:
                                        print(Warning(warning))
                                return warning
        return None


def find(path, folder_keyword, file_keyword, nr_occ=1, exclude_kw=['template', 'exclude']):
        """Search folderstructure for files, return paths containing them.

        Arguments:
        path: string, the path to search
        folder_keyword: strings of the subfolders where the files are supposed to be located
        file_keyword: parts of the filename to be located
        nr_occ: how often the file keyword is supposed to occur in the lowererst folder
        exclude_kw: list of keywords where search should be skipped

        Returns:
        List of strings, a collection of all matching paths

        Example:
        crawl(path='./', folder_keyword='dft', file_keyword='rho', nr_occ=1)
        ['./600_ps_snapshot/2_dft_calculations/rho.cube', 
         './600_ps_snapshot/2_dft_calculations/rho.cube', 
         ...]
        """
        paths = []
        # Crawl the directory structure
        for subdir, dirs, files in sorted(os.walk(path)):

                # Exclude template folders from search
                if any([keyword in subdir for keyword in exclude_kw]):
                        continue

                # Select the folders with the required keyword in them
                if folder_keyword in subdir:

                        # Check if at least one desired file exists
                        if sum([file_keyword in f for f in files]) < 1:
                                print(os.getcwd())
                                raise RuntimeError('No {} file found.'.format(file_keyword))

                        # No more than one file must exists for uniqueness
                        if sum([file_keyword in f for f in files]) > nr_occ:
                                print(os.getcwd())
                                err = 'Multiple files containing {} found.'.format(file_keyword)
                                raise RuntimeError(err)
                                                
                        # If no error was raised, we can use the file we found:
                        for f in files:
                                if file_keyword in f:
                                        paths += [os.path.join(subdir, f)]
        return paths

Functions

def check_existence(path, neccessary_files, verbose=True)

Check if all neccessary files exist in path, print warning for missing files.

Arguments:

path : string, the path to search

 

neccessary_files : list of strings, check if they exist in path

 

verbose : Bool, controls amount of printing

 

Returns: String warning xor None

Source code

def check_existence(path, neccessary_files, verbose=True):
        """Check if all neccessary files exist in path, print warning for missing files.

        Arguments:
        path: string, the path to search
        neccessary_files: list of strings, check if they exist in path
        verbose: Bool, controls amount of printing

        Returns:
        String warning xor None 
        """
        with cd(path):
                # Files should be here
                # if verbose:
                #       print([f for s, d, f in os.walk('.')])

                for f in neccessary_files:
                        if not (os.path.islink(f) or os.path.isfile(f)):
                                warning = 'File not found: {}'.format(f)
                                if verbose:
                                        print(Warning(warning))
                                return warning
        return None

def find(path, folder_keyword, file_keyword, nr_occ=1, exclude_kw=['template', 'exclude'])

Search folderstructure for files, return paths containing them.

Arguments:

path : string, the path to search

 

folder_keyword : strings of the subfolders where the files are supposed to be located

 

file_keyword : parts of the filename to be located

 

nr_occ : how often the file keyword is supposed to occur in the lowererst folder

 

exclude_kw : list of keywords where search should be skipped

 

Returns: List of strings, a collection of all matching paths

Example: crawl(path='./', folder_keyword='dft', file_keyword='rho', nr_occ=1) ['./600_ps_snapshot/2_dft_calculations/rho.cube', './600_ps_snapshot/2_dft_calculations/rho.cube', …]

Source code

def find(path, folder_keyword, file_keyword, nr_occ=1, exclude_kw=['template', 'exclude']):
        """Search folderstructure for files, return paths containing them.

        Arguments:
        path: string, the path to search
        folder_keyword: strings of the subfolders where the files are supposed to be located
        file_keyword: parts of the filename to be located
        nr_occ: how often the file keyword is supposed to occur in the lowererst folder
        exclude_kw: list of keywords where search should be skipped

        Returns:
        List of strings, a collection of all matching paths

        Example:
        crawl(path='./', folder_keyword='dft', file_keyword='rho', nr_occ=1)
        ['./600_ps_snapshot/2_dft_calculations/rho.cube', 
         './600_ps_snapshot/2_dft_calculations/rho.cube', 
         ...]
        """
        paths = []
        # Crawl the directory structure
        for subdir, dirs, files in sorted(os.walk(path)):

                # Exclude template folders from search
                if any([keyword in subdir for keyword in exclude_kw]):
                        continue

                # Select the folders with the required keyword in them
                if folder_keyword in subdir:

                        # Check if at least one desired file exists
                        if sum([file_keyword in f for f in files]) < 1:
                                print(os.getcwd())
                                raise RuntimeError('No {} file found.'.format(file_keyword))

                        # No more than one file must exists for uniqueness
                        if sum([file_keyword in f for f in files]) > nr_occ:
                                print(os.getcwd())
                                err = 'Multiple files containing {} found.'.format(file_keyword)
                                raise RuntimeError(err)
                                                
                        # If no error was raised, we can use the file we found:
                        for f in files:
                                if file_keyword in f:
                                        paths += [os.path.join(subdir, f)]
        return paths

Classes

class cd

Context manager for changing the current working directory

Source code

class cd:
    """Context manager for changing the current working directory"""
    def __init__(self, newPath):
        self.newPath = os.path.expanduser(newPath)

    def __enter__(self):
        self.savedPath = os.getcwd()
        os.chdir(self.newPath)

    def __exit__(self, etype, value, traceback):
        os.chdir(self.savedPath)

Methods

def __init__(self, newPath)

Initialize self. See help(type(self)) for accurate signature.

Source code

def __init__(self, newPath):
    self.newPath = os.path.expanduser(newPath)